Khaled Rasheed

Aravind Mandiga, Guoming Li, Jin Lu et al.

Protein-language systems are often evaluated by whether they generate plausible biological text, but a structural question has a sharper semantics: it denotes a measurement in a 3D coordinate system. We introduce ProtStructQA, an executable benchmark for protein structural question answering in which each natural-language question is generated from a hidden typed domain-specific language (DSL) program and the answer is obtained by executing that program on an AlphaFold-predicted structure. ProtStructQA releases 382.2K questions covering confidence, distances, predicted aligned error (PAE), solvent exposure, secondary structure, topology and contacts, and held-out compositions: a 330K active benchmark over 10K proteins from four species, plus a 52.2K hard-negative robustness pool. Without fine-tuning, we evaluate Qwen3 models from 0.6B to 8B under direct prompting, chain-of-thought, grammar-constrained executable voting, executable voting with chain-of-thought, and multi-turn ReAct-style tool use, and replicate the headline finding on Gemma-3-1B and Gemma-3-12B. We find a capability-dependent denotation threshold between Qwen3-1.7B and Qwen3-4B: below it, tool-mediated ReAct dominates because models often fail to produce executable denotations; above it, chain-of-thought flips from mostly harmful to strongly beneficial and becomes the strongest strategy on most splits. Parse-failure and family-level analyses show that the threshold is a transition from unparseable language to executable structural denotation, while grammar and execution remain selectively valuable for PAE and secondary-structure queries. ProtStructQA reframes scientific QA as compilation from language to measurement and provides a diagnostic testbed for when language models can map words to executable 3D structural measurements.

Mohammadreza Iman, John A. Miller, Khaled Rasheed et al.

Deep transfer learning techniques try to tackle the limitations of deep learning, the dependency on extensive training data and the training costs, by reusing obtained knowledge. However, the current DTL techniques suffer from either catastrophic forgetting dilemma (losing the previously obtained knowledge) or overly biased pre-trained models (harder to adapt to target data) in finetuning pre-trained models or freezing a part of the pre-trained model, respectively. Progressive learning, a sub-category of DTL, reduces the effect of the overly biased model in the case of freezing earlier layers by adding a new layer to the end of a frozen pre-trained model. Even though it has been successful in many cases, it cannot yet handle distant source and target data. We propose a new continual/progressive learning approach for deep transfer learning to tackle these limitations. To avoid both catastrophic forgetting and overly biased-model problems, we expand the pre-trained model by expanding pre-trained layers (adding new nodes to each layer) in the model instead of only adding new layers. Hence the method is named EXPANSE. Our experimental results confirm that we can tackle distant source and target data using this technique. At the same time, the final model is still valid on the source data, achieving a promising deep continual learning approach. Moreover, we offer a new way of training deep learning models inspired by the human education system. We termed this two-step training: learning basics first, then adding complexities and uncertainties. The evaluation implies that the two-step training extracts more meaningful features and a finer basin on the error surface since it can achieve better accuracy in comparison to regular training. EXPANSE (model expansion and two-step training) is a systematic continual learning approach applicable to different problems and DL models.

Zhengliang Liu, Yiwei Li, Qian Cao et al.

Recent advances in artificial general intelligence (AGI), particularly large language models and creative image generation systems have demonstrated impressive capabilities on diverse tasks spanning the arts and humanities. However, the swift evolution of AGI has also raised critical questions about its responsible deployment in these culturally significant domains traditionally seen as profoundly human. This paper provides a comprehensive analysis of the applications and implications of AGI for text, graphics, audio, and video pertaining to arts and the humanities. We survey cutting-edge systems and their usage in areas ranging from poetry to history, marketing to film, and communication to classical art. We outline substantial concerns pertaining to factuality, toxicity, biases, and public safety in AGI systems, and propose mitigation strategies. The paper argues for multi-stakeholder collaboration to ensure AGI promotes creativity, knowledge, and cultural values without undermining truth or human dignity. Our timely contribution summarizes a rapidly developing field, highlighting promising directions while advocating for responsible progress centering on human flourishing. The analysis lays the groundwork for further research on aligning AGI's technological capacities with enduring social goods.

Sahar Voghoei, James Byars, John A Miller et al.

This paper proposes a model to predict the levels (e.g., Bachelor, Master, etc.) of postsecondary degree awards that have been ambiguously expressed in the student tracking reports of the National Student Clearinghouse (NSC). The model will be the hybrid of two modules. The first module interprets the relevant abbreviatory elements embedded in NSC reports by referring to a comprehensive database that we have made of nearly 950 abbreviations for degree titles used by American postsecondary educators. The second module is a combination of feature classification and text mining modeled with CNN-BiLSTM, which is preceded by several steps of heavy pre-processing. The model proposed in this paper was trained with four multi-label datasets of different grades of resolution and returned 97.83\% accuracy with the most sophisticated dataset. Such a thorough classification of degree levels will provide insights into the modeling patterns of student success and mobility. To date, such a classification strategy has not been attempted except using manual methods and simple text parsing logic.

Jonathan Vance, Khaled Rasheed, Ali Missaoui et al.

The alfalfa crop is globally important as livestock feed, so highly efficient planting and harvesting could benefit many industries, especially as the global climate changes and traditional methods become less accurate. Recent work using machine learning (ML) to predict yields for alfalfa and other crops has shown promise. Previous efforts used remote sensing, weather, planting, and soil data to train machine learning models for yield prediction. However, while remote sensing works well, the models require large amounts of data and cannot make predictions until the harvesting season begins. Using weather and planting data from alfalfa variety trials in Kentucky and Georgia, our previous work compared feature selection techniques to find the best technique and best feature set. In this work, we trained a variety of machine learning models, using cross validation for hyperparameter optimization, to predict biomass yields, and we showed better accuracy than similar work that employed more complex techniques. Our best individual model was a random forest with a mean absolute error of 0.081 tons/acre and R{$^2$} of 0.941. Next, we expanded this dataset to include Wisconsin and Mississippi, and we repeated our experiments, obtaining a higher best R{$^2$} of 0.982 with a regression tree. We then isolated our testing datasets by state to explore this problem's eligibility for domain adaptation (DA), as we trained on multiple source states and tested on one target state. This Trivial DA (TDA) approach leaves plenty of room for improvement through exploring more complex DA techniques in forthcoming work.

Khalifeh AlJadda, Rene Ranzinger, Melody Porterfield et al.

Several algorithms and tools have been developed to (semi) automate the process of glycan identification by interpreting Mass Spectrometric data. However, each has limitations when annotating MSn data with thousands of MS spectra using uncurated public databases. Moreover, the existing tools are not designed to manage MSn data where n > 2. We propose a novel software package to automate the annotation of tandem MS data. This software consists of two major components. The first, is a free, semi-automated MSn data interpreter called the Glycomic Elucidation and Annotation Tool (GELATO). This tool extends and automates the functionality of existing open source projects, namely, GlycoWorkbench (GWB) and GlycomeDB. The second is a machine learning model called Smart Anotation Enhancement Graph (SAGE), which learns the behavior of glycoanalysts to select annotations generated by GELATO that emulate human interpretation of the spectra.

Farid Ghareh Mohammadi, Farzan Shenavarmasouleh, Khaled Rasheed et al.

In the past 30 years, scientists have searched nature, including animals and insects, and biology in order to discover, understand, and model solutions for solving large-scale science challenges. The study of bionics reveals that how the biological structures, functions found in nature have improved our modern technologies. In this study, we present our discovery of evolutionary and nature-inspired algorithms applications in Data Science and Data Analytics in three main topics of pre-processing, supervised algorithms, and unsupervised algorithms. Among all applications, in this study, we aim to investigate four optimization algorithms that have been performed using the evolutionary and nature-inspired algorithms within data science and analytics. Feature selection optimization in pre-processing section, Hyper-parameter tuning optimization, and knowledge discovery optimization in supervised algorithms, and clustering optimization in the unsupervised algorithms.

Soheyla Amirian, Thiab R. Taha, Khaled Rasheed et al.

Physical computing infrastructure, data gathering, and algorithms have recently had significant advances to extract information from images and videos. The growth has been especially outstanding in image captioning and video captioning. However, most of the advancements in video captioning still take place in short videos. In this research, we caption longer videos only by using the keyframes, which are a small subset of the total video frames. Instead of processing thousands of frames, only a few frames are processed depending on the number of keyframes. There is a trade-off between the computation of many frames and the speed of the captioning process. The approach in this research is to allow the user to specify the trade-off between execution time and accuracy. In addition, we argue that linking images, videos, and natural language offers many practical benefits and immediate practical applications. From the modeling perspective, instead of designing and staging explicit algorithms to process videos and generate captions in complex processing pipelines, our contribution lies in designing hybrid deep learning architectures to apply in long videos by captioning video keyframes. We consider the technology and the methodology that we have developed as steps toward the applications discussed in this research.

Soheyla Amirian, Thiab R. Taha, Khaled Rasheed et al.

Generative Adversarial Networks (GANs) are machine learning methods that are used in many important and novel applications. For example, in imaging science, GANs are effectively utilized in generating image datasets, photographs of human faces, image and video captioning, image-to-image translation, text-to-image translation, video prediction, and 3D object generation to name a few. In this paper, we discuss how GANs can be used to create an artificial world. More specifically, we discuss how GANs help to describe an image utilizing image/video captioning methods and how to translate the image to a new image using image-to-image translation frameworks in a theme we desire. We articulate how GANs impact creating a customized world.

Mohammadreza Iman, Khaled Rasheed, Hamid R. Arabnia

Deep learning has been the answer to many machine learning problems during the past two decades. However, it comes with two major constraints: dependency on extensive labeled data and training costs. Transfer learning in deep learning, known as Deep Transfer Learning (DTL), attempts to reduce such dependency and costs by reusing an obtained knowledge from a source data/task in training on a target data/task. Most applied DTL techniques are network/model-based approaches. These methods reduce the dependency of deep learning models on extensive training data and drastically decrease training costs. As a result, researchers detected Covid-19 infection on chest X-Rays with high accuracy at the beginning of the pandemic with minimal data using DTL techniques. Also, the training cost reduction makes DTL viable on edge devices with limited resources. Like any new advancement, DTL methods have their own limitations, and a successful transfer depends on some adjustments for different scenarios. In this paper, we review the definition and taxonomy of deep transfer learning and well-known methods. Then we investigate the DTL approaches by reviewing recent applied DTL techniques in the past five years. Further, we review some experimental analyses of DTLs to learn the best practice for applying DTL in different scenarios. Moreover, the limitations of DTLs (catastrophic forgetting dilemma and overly biased pre-trained models) are discussed, along with possible solutions and research trends.

Farzan Shenavarmasouleh, Farid Ghareh Mohammadi, M. Hadi Amini et al.

Medical Imaging is one of the growing fields in the world of computer vision. In this study, we aim to address the Diabetic Retinopathy (DR) problem as one of the open challenges in medical imaging. In this research, we propose a new lesion detection architecture, comprising of two sub-modules, which is an optimal solution to detect and find not only the type of lesions caused by DR, their corresponding bounding boxes, and their masks; but also the severity level of the overall case. Aside from traditional accuracy, we also use two popular evaluation criteria to evaluate the outputs of our models, which are intersection over union (IOU) and mean average precision (mAP). We hypothesize that this new solution enables specialists to detect lesions with high confidence and estimate the severity of the damage with high accuracy.

Hamed Yaghoobian, Hamid R. Arabnia, Khaled Rasheed

Sarcasm detection is the task of identifying irony containing utterances in sentiment-bearing text. However, the figurative and creative nature of sarcasm poses a great challenge for affective computing systems performing sentiment analysis. This article compiles and reviews the salient work in the literature of automatic sarcasm detection. Thus far, three main paradigm shifts have occurred in the way researchers have approached this task: 1) semi-supervised pattern extraction to identify implicit sentiment, 2) use of hashtag-based supervision, and 3) incorporation of context beyond target text. In this article, we provide a comprehensive review of the datasets, approaches, trends, and issues in sarcasm and irony detection.

Soheyla Amirian, Khaled Rasheed, Thiab R. Taha et al.

Over the last decade, the use of Deep Learning in many applications produced results that are comparable to and in some cases surpassing human expert performance. The application domains include diagnosing diseases, finance, agriculture, search engines, robot vision, and many others. In this paper, we are proposing an architecture that utilizes image/video captioning methods and Natural Language Processing systems to generate a title and a concise abstract for a video. Such a system can potentially be utilized in many application domains, including, the cinema industry, video search engines, security surveillance, video databases/warehouses, data centers, and others. The proposed system functions and operates as followed: it reads a video; representative image frames are identified and selected; the image frames are captioned; NLP is applied to all generated captions together with text summarization; and finally, a title and an abstract are generated for the video. All functions are performed automatically. Preliminary results are provided in this paper using publicly available datasets. This paper is not concerned about the efficiency of the system at the execution time. We hope to be able to address execution efficiency issues in our subsequent publications.

Soheyla Amirian, Abolfazl Farahani, Hamid R. Arabnia et al.

Video Captioning is considered to be one of the most challenging problems in the field of computer vision. Video Captioning involves the combination of different deep learning models to perform object detection, action detection, and localization by processing a sequence of image frames. It is crucial to consider the sequence of actions in a video in order to generate a meaningful description of the overall action event. A reliable, accurate, and real-time video captioning method can be used in many applications. However, this paper focuses on one application: video captioning for fostering and facilitating physical activities. In broad terms, the work can be considered to be assistive technology. Lack of physical activity appears to be increasingly widespread in many nations due to many factors, the most important being the convenience that technology has provided in workplaces. The adopted sedentary lifestyle is becoming a significant public health issue. Therefore, it is essential to incorporate more physical movements into our daily lives. Tracking one's daily physical activities would offer a base for comparison with activities performed in subsequent days. With the above in mind, this paper proposes a video captioning framework that aims to describe the activities in a video and estimate a person's daily physical activity level. This framework could potentially help people trace their daily movements to reduce an inactive lifestyle's health risks. The work presented in this paper is still in its infancy. The initial steps of the application are outlined in this paper. Based on our preliminary research, this project has great merit.

Abolfazl Farahani, Behrouz Pourshojae, Khaled Rasheed et al.

The availability of abundant labeled data in recent years led the researchers to introduce a methodology called transfer learning, which utilizes existing data in situations where there are difficulties in collecting new annotated data. Transfer learning aims to boost the performance of a target learner by applying another related source data. In contrast to the traditional machine learning and data mining techniques, which assume that the training and testing data lie from the same feature space and distribution, transfer learning can handle situations where there is a discrepancy between domains and distributions. These characteristics give the model the potential to utilize the available related source data and extend the underlying knowledge to the target task achieving better performance. This survey paper aims to give a concise review of traditional and current transfer learning settings, existing challenges, and related approaches.

Abolfazl Farahani, Sahar Voghoei, Khaled Rasheed et al.

Classical machine learning assumes that the training and test sets come from the same distributions. Therefore, a model learned from the labeled training data is expected to perform well on the test data. However, This assumption may not always hold in real-world applications where the training and the test data fall from different distributions, due to many factors, e.g., collecting the training and test sets from different sources, or having an out-dated training set due to the change of data over time. In this case, there would be a discrepancy across domain distributions, and naively applying the trained model on the new dataset may cause degradation in the performance. Domain adaptation is a sub-field within machine learning that aims to cope with these types of problems by aligning the disparity between domains such that the trained model can be generalized into the domain of interest. This paper focuses on unsupervised domain adaptation, where the labels are only available in the source domain. It addresses the categorization of domain adaptation from different viewpoints. Besides, It presents some successful shallow and deep domain adaptation approaches that aim to deal with domain adaptation problems.

Mohammadreza Iman, Amy Giuntini, Hamid Reza Arabnia et al.

People with Parkinson's disease must be regularly monitored by their physician to observe how the disease is progressing and potentially adjust treatment plans to mitigate the symptoms. Monitoring the progression of the disease through a voice recording captured by the patient at their own home can make the process faster and less stressful. Using a dataset of voice recordings of 42 people with early-stage Parkinson's disease over a time span of 6 months, we applied multiple machine learning techniques to find a correlation between the voice recording and the patient's motor UPDRS score. We approached this problem using a multitude of both regression and classification techniques. Much of this paper is dedicated to mapping the voice data to motor UPDRS scores using regression techniques in order to obtain a more precise value for unknown instances. Through this comparative study of variant machine learning methods, we realized some old machine learning methods like trees outperform cutting edge deep learning models on numerous tabular datasets.

Khalifeh AlJadda, Mohammed Korayem, Camilo Ortiz et al.

Probabilistic Graphical Models (PGM) are very useful in the fields of machine learning and data mining. The crucial limitation of those models,however, is the scalability. The Bayesian Network, which is one of the most common PGMs used in machine learning and data mining, demonstrates this limitation when the training data consists of random variables, each of them has a large set of possible values. In the big data era, one would expect new extensions to the existing PGMs to handle the massive amount of data produced these days by computers, sensors and other electronic devices. With hierarchical data - data that is arranged in a treelike structure with several levels - one would expect to see hundreds of thousands or millions of values distributed over even just a small number of levels. When modeling this kind of hierarchical data across large data sets, Bayesian Networks become infeasible for representing the probability distributions. In this paper we introduce an extension to Bayesian Networks to handle massive sets of hierarchical data in a reasonable amount of time and space. The proposed model achieves perfect precision of 1.0 and high recall of 0.93 when it is used as multi-label classifier for the annotation of mass spectrometry data. On another data set of 1.5 billion search logs provided by CareerBuilder.com the model was able to predict latent semantic relationships between search keywords with accuracy up to 0.80.